Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 986,275 G→T 28.4% S172S (TCG→TCT)  ynfE → oxidoreductase subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE986,2750GT28.4% 178.5 / 66.4 123S172S (TCG→TCT) ynfEoxidoreductase subunit
Reads supporting (aligned to +/- strand):  ref base G (40/48);  new base T (12/23);  total (52/71)
Fisher's exact test for biased strand distribution p-value = 3.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.26e-01

Only 100 of 124 total aligned reads displayed.

ATGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAGTATGGC  >  minE/986208‑986338
                                                                   |                                                               
atGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCg                                                                 >  1:2615386/1‑68 (MQ=255)
atGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGc                                                                >  1:982644/1‑69 (MQ=255)
atGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGc                                                                >  1:2059266/1‑69 (MQ=255)
atGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGc                                                                >  1:264010/1‑69 (MQ=255)
atGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGc                                                                >  1:2138223/1‑69 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggctg                                                 <  1:2484088/67‑3 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1533385/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:3402034/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:607665/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:2439650/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:2290297/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:700753/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1693056/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1779022/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1969549/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1905572/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1897522/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1392613/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:2894328/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1142105/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:386132/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:989995/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:1071952/67‑1 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTcggcgg                                                 >  1:1115810/1‑67 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGt                                                >  1:1349599/1‑68 (MQ=255)
                 tatatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGt                                                >  1:114489/1‑68 (MQ=255)
                   tatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCa                                              <  1:2986539/68‑1 (MQ=255)
                   tatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCa                                              <  1:456043/68‑1 (MQ=255)
                   tatTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCa                                              <  1:3278377/68‑1 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGcc                                                               >  1:1036038/1‑49 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGGGGTCAAAc                                           >  1:3228586/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAAc                                           >  1:550656/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAAc                                           >  1:1577636/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAAc                                           >  1:3181749/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAAc                                           >  1:2659349/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGGCAAAc                                           >  1:948631/1‑69 (MQ=255)
                     ttCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGAGGTCAAAc                                           >  1:1199870/1‑69 (MQ=255)
                          tACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtg                                      >  1:2951468/1‑69 (MQ=255)
                          tACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtg                                      >  1:692686/1‑69 (MQ=255)
                          tACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtg                                      >  1:2915213/1‑69 (MQ=255)
                          tACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCt                                       >  1:2122670/1‑68 (MQ=255)
                          tACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCt                                       >  1:3087930/1‑68 (MQ=255)
                              ctTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtgatga                                  <  1:155164/69‑1 (MQ=255)
                              ctTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtgatga                                  <  1:2706781/69‑1 (MQ=255)
                              ctTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtgatga                                  <  1:851754/69‑1 (MQ=255)
                              ctTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCtgatga                                  <  1:1954604/69‑1 (MQ=255)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:805392/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:12330/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:2927977/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:1197702/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:2355338/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:2243434/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:1657924/1‑40 (MQ=38)
                               ttCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCa                                                              >  1:3246379/1‑40 (MQ=38)
                                tCGGGGATTGTTGGCGGCAATATGACCCGCTCTTCTCCATCAGCCTcggcgg                                                 <  1:2386024/52‑1 (MQ=39)
                                     gATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTa                           >  1:3114787/1‑69 (MQ=255)
                                           tGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTAcggcgg                     <  1:226278/69‑1 (MQ=255)
                                           tGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTAcggcgg                     <  1:295218/69‑1 (MQ=255)
                                           tGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTAcggcgg                     <  1:2173950/69‑1 (MQ=255)
                                           tGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTAcggcgg                     <  1:1690618/69‑1 (MQ=255)
                                           tGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTAcggcgg                     <  1:2053616/69‑1 (MQ=255)
                                                gcAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCa                 >  1:1138108/1‑68 (MQ=255)
                                                gcAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCa                 >  1:1290033/1‑68 (MQ=255)
                                                gcAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCa                 >  1:716037/1‑68 (MQ=255)
                                                gcAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCa                 >  1:2346216/1‑68 (MQ=255)
                                                gcAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCa                 >  1:2489246/1‑68 (MQ=255)
                                                   atatGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCa             <  1:120801/69‑1 (MQ=255)
                                                   atatGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCa             <  1:2916159/69‑1 (MQ=255)
                                                   atatGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCa             <  1:2271257/69‑1 (MQ=255)
                                                     atGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCa             >  1:3389476/1‑67 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:2389655/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:182914/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:3165583/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:2653729/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:179263/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:1148244/1‑69 (MQ=255)
                                                      tGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAAcc          >  1:56554/1‑69 (MQ=255)
                                                        aCCCTCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1571137/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:702643/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:990400/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:552149/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2117967/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1038100/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1337301/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1633606/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1794091/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1820797/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1984764/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2023467/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2506785/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2566608/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2699751/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2710976/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:2793044/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:3067774/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:3289842/69‑1 (MQ=255)
                                                        aCCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:3338029/69‑1 (MQ=255)
                                                         cccGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:746239/68‑1 (MQ=255)
                                                              tctTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAg        <  1:1089475/63‑1 (MQ=255)
                                                              tctTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAGTATGGc  <  1:3355421/69‑1 (MQ=255)
                                                                   |                                                               
ATGGCAATGAGGCTGTATATATTCAGTACTCTTCGGGGATCGTTGGCGGCAATATGACCCGCTCTTCGCCATCAGCCTCGGCGGTCAAACGCCTGATGAACTGCTACGGCGGTTCACTCAACCAGTATGGC  >  minE/986208‑986338

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A